Re: [AMBER] non zero net charge on molecule from AM1-BCC charge parameter fit

From: Jason Swails <>
Date: Wed, 4 May 2016 21:01:47 -0400

On Wed, May 4, 2016 at 3:54 PM, conor parks <> wrote:

> Thanks thomas,
> I would like to clarify what you mean by smearing. If my net charge is
> -0.001e, and I want to smear them onto the methyl hydrogens, am I correct
> in assuming you mean subtract -0.001/3 from the charges on the methyl
> hydrogens? Is there any way to determine if its better to smear onto the
> methyl hydrogens or the HO hydrogen?

​I recently dealt with precisely this problem in ParmEd. The algorithm I
chose was to divide up the difference between the target charge (some
integer) and the actual charge, divide it evenly between the atoms, then
round each charge to the precision I was going to print it out in the mol2
file. This could once again lead to a slightly non-neutral charge, but it
would be off by no more than 0.000001 (or 0.0001 if I wrote it out to 4
decimal places). Then I just added that extra negligible fraction to the
first atom.

That's way more than you need to do, though. Charges between different
conformers of the same molecule will differ by more than 0.001 electrons,
so if you wanted to you could just add that value to any atom in the system
and it would not make a measurable difference.​

​A charge of 0.001 is nearing the highest level of precision with which you
can determine charges using very careful, multi-conformational RESP fits
with many conformations, so this extra amount of charge will disappear into
the noise no matter where you put it.


Jason M. Swails
AMBER mailing list
Received on Wed May 04 2016 - 18:30:04 PDT
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